Past Events

How to set up a Protein Simulation, 2nd edition
Wednesday 20 March 2013

This workshop is aimed at beginners wishing to learn the practicalities of setting up a protein molecular dynamics simulation.


Unilever Centre for Molecular Informatics, University of Cambridge


Syma Khalid (Southampton)
Peter Bond (Cambridge)

The workshop will be focussed on the three main challenges of setting up a simulation:

  1. Preparing your protein for simulations, to include: missing atoms/residues; protonation states; unusual geometries.
  2. Adding ions and solvent, to include: which ions to use; ion placement; solvent types etc.
  3. Equilibration and simulation, to include: strategies for checking the system has relaxed and set-ups for different types of system.

It will also cover basic analysis techniques. The principles for these challenges are the same whatever simulation software is used, however during the hands-on sessions the workshop will focus on the GROMACS simulation package.

Some knowledge of the Linux operating system is desirable, but not essential. The workshop is aimed at, although not restricted to, first/second year PhD students.

The one-day workshop is likely to start at 10am and be finished by 5pm. A more detailed programme will be available soon.

Registration - deadline 8th March

There is no charge for the workshop, although there are only 21 places available, so we recommend early registration to avoid disappointment. Please register here. Once you have registered for the workshop, registrations will pass through a selection process. We have opened registration up to 50 people to express initial interest at this stage. Once the selection process is complete, successful applicants will be notified by email. Priority will be given to UK students.


Although we do not provide accommodation for this workshop we would recommend the following hotels for anyone that requires an overnight stay.

Royal Cambridge Hotel (
Lensfield Hotel (

Alternatively, "Conference Cambridge" provides details of available college accommodation (

All delegates are responsible for making their own bookings.